482 lines
20 KiB
Python
482 lines
20 KiB
Python
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from os import path
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import warnings
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import numpy as np
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from numpy.testing import (assert_equal, assert_array_equal,
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assert_, suppress_warnings)
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import pytest
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from scipy.io import readsav
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from scipy.io import _idl
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DATA_PATH = path.join(path.dirname(__file__), 'data')
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def assert_identical(a, b):
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"""Assert whether value AND type are the same"""
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assert_equal(a, b)
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if isinstance(b, str):
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assert_equal(type(a), type(b))
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else:
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assert_equal(np.asarray(a).dtype.type, np.asarray(b).dtype.type)
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def assert_array_identical(a, b):
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"""Assert whether values AND type are the same"""
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assert_array_equal(a, b)
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assert_equal(a.dtype.type, b.dtype.type)
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# Define vectorized ID function for pointer arrays
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vect_id = np.vectorize(id)
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class TestIdict:
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def test_idict(self):
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custom_dict = {'a': np.int16(999)}
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original_id = id(custom_dict)
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s = readsav(path.join(DATA_PATH, 'scalar_byte.sav'),
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idict=custom_dict, verbose=False)
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assert_equal(original_id, id(s))
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assert_('a' in s)
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assert_identical(s['a'], np.int16(999))
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assert_identical(s['i8u'], np.uint8(234))
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class TestScalars:
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# Test that scalar values are read in with the correct value and type
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def test_byte(self):
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s = readsav(path.join(DATA_PATH, 'scalar_byte.sav'), verbose=False)
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assert_identical(s.i8u, np.uint8(234))
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def test_int16(self):
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s = readsav(path.join(DATA_PATH, 'scalar_int16.sav'), verbose=False)
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assert_identical(s.i16s, np.int16(-23456))
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def test_int32(self):
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s = readsav(path.join(DATA_PATH, 'scalar_int32.sav'), verbose=False)
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assert_identical(s.i32s, np.int32(-1234567890))
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def test_float32(self):
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s = readsav(path.join(DATA_PATH, 'scalar_float32.sav'), verbose=False)
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assert_identical(s.f32, np.float32(-3.1234567e+37))
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def test_float64(self):
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s = readsav(path.join(DATA_PATH, 'scalar_float64.sav'), verbose=False)
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assert_identical(s.f64, np.float64(-1.1976931348623157e+307))
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def test_complex32(self):
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s = readsav(path.join(DATA_PATH, 'scalar_complex32.sav'), verbose=False)
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assert_identical(s.c32, np.complex64(3.124442e13-2.312442e31j))
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def test_bytes(self):
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s = readsav(path.join(DATA_PATH, 'scalar_string.sav'), verbose=False)
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msg = "The quick brown fox jumps over the lazy python"
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assert_identical(s.s, np.bytes_(msg))
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def test_structure(self):
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pass
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def test_complex64(self):
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s = readsav(path.join(DATA_PATH, 'scalar_complex64.sav'), verbose=False)
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assert_identical(
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s.c64,
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np.complex128(1.1987253647623157e+112-5.1987258887729157e+307j)
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)
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def test_heap_pointer(self):
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pass
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def test_object_reference(self):
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pass
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def test_uint16(self):
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s = readsav(path.join(DATA_PATH, 'scalar_uint16.sav'), verbose=False)
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assert_identical(s.i16u, np.uint16(65511))
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def test_uint32(self):
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s = readsav(path.join(DATA_PATH, 'scalar_uint32.sav'), verbose=False)
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assert_identical(s.i32u, np.uint32(4294967233))
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def test_int64(self):
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s = readsav(path.join(DATA_PATH, 'scalar_int64.sav'), verbose=False)
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assert_identical(s.i64s, np.int64(-9223372036854774567))
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def test_uint64(self):
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s = readsav(path.join(DATA_PATH, 'scalar_uint64.sav'), verbose=False)
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assert_identical(s.i64u, np.uint64(18446744073709529285))
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class TestCompressed(TestScalars):
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# Test that compressed .sav files can be read in
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def test_compressed(self):
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s = readsav(path.join(DATA_PATH, 'various_compressed.sav'), verbose=False)
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assert_identical(s.i8u, np.uint8(234))
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assert_identical(s.f32, np.float32(-3.1234567e+37))
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assert_identical(
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s.c64,
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np.complex128(1.1987253647623157e+112-5.1987258887729157e+307j)
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)
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assert_equal(s.array5d.shape, (4, 3, 4, 6, 5))
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assert_identical(s.arrays.a[0], np.array([1, 2, 3], dtype=np.int16))
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assert_identical(s.arrays.b[0], np.array([4., 5., 6., 7.], dtype=np.float32))
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assert_identical(s.arrays.c[0],
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np.array([np.complex64(1+2j), np.complex64(7+8j)]))
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assert_identical(s.arrays.d[0],
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np.array([b"cheese", b"bacon", b"spam"], dtype=object))
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class TestArrayDimensions:
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# Test that multi-dimensional arrays are read in with the correct dimensions
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def test_1d(self):
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s = readsav(path.join(DATA_PATH, 'array_float32_1d.sav'), verbose=False)
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assert_equal(s.array1d.shape, (123, ))
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def test_2d(self):
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s = readsav(path.join(DATA_PATH, 'array_float32_2d.sav'), verbose=False)
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assert_equal(s.array2d.shape, (22, 12))
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def test_3d(self):
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s = readsav(path.join(DATA_PATH, 'array_float32_3d.sav'), verbose=False)
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assert_equal(s.array3d.shape, (11, 22, 12))
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def test_4d(self):
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s = readsav(path.join(DATA_PATH, 'array_float32_4d.sav'), verbose=False)
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assert_equal(s.array4d.shape, (4, 5, 8, 7))
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def test_5d(self):
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s = readsav(path.join(DATA_PATH, 'array_float32_5d.sav'), verbose=False)
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assert_equal(s.array5d.shape, (4, 3, 4, 6, 5))
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def test_6d(self):
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s = readsav(path.join(DATA_PATH, 'array_float32_6d.sav'), verbose=False)
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assert_equal(s.array6d.shape, (3, 6, 4, 5, 3, 4))
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def test_7d(self):
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s = readsav(path.join(DATA_PATH, 'array_float32_7d.sav'), verbose=False)
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assert_equal(s.array7d.shape, (2, 1, 2, 3, 4, 3, 2))
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def test_8d(self):
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s = readsav(path.join(DATA_PATH, 'array_float32_8d.sav'), verbose=False)
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assert_equal(s.array8d.shape, (4, 3, 2, 1, 2, 3, 5, 4))
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class TestStructures:
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def test_scalars(self):
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s = readsav(path.join(DATA_PATH, 'struct_scalars.sav'), verbose=False)
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assert_identical(s.scalars.a, np.array(np.int16(1)))
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assert_identical(s.scalars.b, np.array(np.int32(2)))
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assert_identical(s.scalars.c, np.array(np.float32(3.)))
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assert_identical(s.scalars.d, np.array(np.float64(4.)))
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assert_identical(s.scalars.e, np.array([b"spam"], dtype=object))
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assert_identical(s.scalars.f, np.array(np.complex64(-1.+3j)))
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def test_scalars_replicated(self):
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s = readsav(path.join(DATA_PATH, 'struct_scalars_replicated.sav'),
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verbose=False)
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assert_identical(s.scalars_rep.a, np.repeat(np.int16(1), 5))
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assert_identical(s.scalars_rep.b, np.repeat(np.int32(2), 5))
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assert_identical(s.scalars_rep.c, np.repeat(np.float32(3.), 5))
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assert_identical(s.scalars_rep.d, np.repeat(np.float64(4.), 5))
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assert_identical(s.scalars_rep.e, np.repeat(b"spam", 5).astype(object))
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assert_identical(s.scalars_rep.f, np.repeat(np.complex64(-1.+3j), 5))
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def test_scalars_replicated_3d(self):
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s = readsav(path.join(DATA_PATH, 'struct_scalars_replicated_3d.sav'),
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verbose=False)
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assert_identical(s.scalars_rep.a, np.repeat(np.int16(1), 24).reshape(4, 3, 2))
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assert_identical(s.scalars_rep.b, np.repeat(np.int32(2), 24).reshape(4, 3, 2))
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assert_identical(s.scalars_rep.c,
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np.repeat(np.float32(3.), 24).reshape(4, 3, 2))
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assert_identical(s.scalars_rep.d,
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np.repeat(np.float64(4.), 24).reshape(4, 3, 2))
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assert_identical(s.scalars_rep.e,
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np.repeat(b"spam", 24).reshape(4, 3, 2).astype(object))
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assert_identical(s.scalars_rep.f,
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np.repeat(np.complex64(-1.+3j), 24).reshape(4, 3, 2))
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def test_arrays(self):
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s = readsav(path.join(DATA_PATH, 'struct_arrays.sav'), verbose=False)
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assert_array_identical(s.arrays.a[0], np.array([1, 2, 3], dtype=np.int16))
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assert_array_identical(s.arrays.b[0],
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np.array([4., 5., 6., 7.], dtype=np.float32))
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assert_array_identical(s.arrays.c[0],
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np.array([np.complex64(1+2j), np.complex64(7+8j)]))
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assert_array_identical(s.arrays.d[0],
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np.array([b"cheese", b"bacon", b"spam"], dtype=object))
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def test_arrays_replicated(self):
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s = readsav(path.join(DATA_PATH, 'struct_arrays_replicated.sav'), verbose=False)
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# Check column types
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assert_(s.arrays_rep.a.dtype.type is np.object_)
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assert_(s.arrays_rep.b.dtype.type is np.object_)
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assert_(s.arrays_rep.c.dtype.type is np.object_)
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assert_(s.arrays_rep.d.dtype.type is np.object_)
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# Check column shapes
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assert_equal(s.arrays_rep.a.shape, (5, ))
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assert_equal(s.arrays_rep.b.shape, (5, ))
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assert_equal(s.arrays_rep.c.shape, (5, ))
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assert_equal(s.arrays_rep.d.shape, (5, ))
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# Check values
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for i in range(5):
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assert_array_identical(s.arrays_rep.a[i],
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np.array([1, 2, 3], dtype=np.int16))
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assert_array_identical(s.arrays_rep.b[i],
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np.array([4., 5., 6., 7.], dtype=np.float32))
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assert_array_identical(s.arrays_rep.c[i],
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np.array([np.complex64(1+2j),
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np.complex64(7+8j)]))
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assert_array_identical(s.arrays_rep.d[i],
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np.array([b"cheese", b"bacon", b"spam"],
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dtype=object))
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def test_arrays_replicated_3d(self):
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s = readsav(path.join(DATA_PATH, 'struct_arrays_replicated_3d.sav'),
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verbose=False)
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# Check column types
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assert_(s.arrays_rep.a.dtype.type is np.object_)
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assert_(s.arrays_rep.b.dtype.type is np.object_)
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assert_(s.arrays_rep.c.dtype.type is np.object_)
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assert_(s.arrays_rep.d.dtype.type is np.object_)
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# Check column shapes
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assert_equal(s.arrays_rep.a.shape, (4, 3, 2))
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assert_equal(s.arrays_rep.b.shape, (4, 3, 2))
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assert_equal(s.arrays_rep.c.shape, (4, 3, 2))
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assert_equal(s.arrays_rep.d.shape, (4, 3, 2))
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# Check values
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for i in range(4):
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for j in range(3):
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for k in range(2):
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assert_array_identical(s.arrays_rep.a[i, j, k],
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np.array([1, 2, 3], dtype=np.int16))
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assert_array_identical(s.arrays_rep.b[i, j, k],
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np.array([4., 5., 6., 7.],
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dtype=np.float32))
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assert_array_identical(s.arrays_rep.c[i, j, k],
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np.array([np.complex64(1+2j),
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np.complex64(7+8j)]))
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assert_array_identical(s.arrays_rep.d[i, j, k],
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np.array([b"cheese", b"bacon", b"spam"],
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dtype=object))
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def test_inheritance(self):
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s = readsav(path.join(DATA_PATH, 'struct_inherit.sav'), verbose=False)
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assert_identical(s.fc.x, np.array([0], dtype=np.int16))
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assert_identical(s.fc.y, np.array([0], dtype=np.int16))
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assert_identical(s.fc.r, np.array([0], dtype=np.int16))
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assert_identical(s.fc.c, np.array([4], dtype=np.int16))
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def test_arrays_corrupt_idl80(self):
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# test byte arrays with missing nbyte information from IDL 8.0 .sav file
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with suppress_warnings() as sup:
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sup.filter(UserWarning, "Not able to verify number of bytes from header")
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s = readsav(path.join(DATA_PATH,'struct_arrays_byte_idl80.sav'),
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verbose=False)
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assert_identical(s.y.x[0], np.array([55,66], dtype=np.uint8))
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class TestPointers:
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# Check that pointers in .sav files produce references to the same object in Python
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def test_pointers(self):
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s = readsav(path.join(DATA_PATH, 'scalar_heap_pointer.sav'), verbose=False)
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assert_identical(
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s.c64_pointer1,
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np.complex128(1.1987253647623157e+112-5.1987258887729157e+307j)
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)
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assert_identical(
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s.c64_pointer2,
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np.complex128(1.1987253647623157e+112-5.1987258887729157e+307j)
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)
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assert_(s.c64_pointer1 is s.c64_pointer2)
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class TestPointerArray:
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# Test that pointers in arrays are correctly read in
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def test_1d(self):
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s = readsav(path.join(DATA_PATH, 'array_float32_pointer_1d.sav'), verbose=False)
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assert_equal(s.array1d.shape, (123, ))
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|
|
assert_(np.all(s.array1d == np.float32(4.)))
|
||
|
|
assert_(np.all(vect_id(s.array1d) == id(s.array1d[0])))
|
||
|
|
|
||
|
|
def test_2d(self):
|
||
|
|
s = readsav(path.join(DATA_PATH, 'array_float32_pointer_2d.sav'), verbose=False)
|
||
|
|
assert_equal(s.array2d.shape, (22, 12))
|
||
|
|
assert_(np.all(s.array2d == np.float32(4.)))
|
||
|
|
assert_(np.all(vect_id(s.array2d) == id(s.array2d[0,0])))
|
||
|
|
|
||
|
|
def test_3d(self):
|
||
|
|
s = readsav(path.join(DATA_PATH, 'array_float32_pointer_3d.sav'), verbose=False)
|
||
|
|
assert_equal(s.array3d.shape, (11, 22, 12))
|
||
|
|
assert_(np.all(s.array3d == np.float32(4.)))
|
||
|
|
assert_(np.all(vect_id(s.array3d) == id(s.array3d[0,0,0])))
|
||
|
|
|
||
|
|
def test_4d(self):
|
||
|
|
s = readsav(path.join(DATA_PATH, 'array_float32_pointer_4d.sav'), verbose=False)
|
||
|
|
assert_equal(s.array4d.shape, (4, 5, 8, 7))
|
||
|
|
assert_(np.all(s.array4d == np.float32(4.)))
|
||
|
|
assert_(np.all(vect_id(s.array4d) == id(s.array4d[0,0,0,0])))
|
||
|
|
|
||
|
|
def test_5d(self):
|
||
|
|
s = readsav(path.join(DATA_PATH, 'array_float32_pointer_5d.sav'), verbose=False)
|
||
|
|
assert_equal(s.array5d.shape, (4, 3, 4, 6, 5))
|
||
|
|
assert_(np.all(s.array5d == np.float32(4.)))
|
||
|
|
assert_(np.all(vect_id(s.array5d) == id(s.array5d[0,0,0,0,0])))
|
||
|
|
|
||
|
|
def test_6d(self):
|
||
|
|
s = readsav(path.join(DATA_PATH, 'array_float32_pointer_6d.sav'), verbose=False)
|
||
|
|
assert_equal(s.array6d.shape, (3, 6, 4, 5, 3, 4))
|
||
|
|
assert_(np.all(s.array6d == np.float32(4.)))
|
||
|
|
assert_(np.all(vect_id(s.array6d) == id(s.array6d[0,0,0,0,0,0])))
|
||
|
|
|
||
|
|
def test_7d(self):
|
||
|
|
s = readsav(path.join(DATA_PATH, 'array_float32_pointer_7d.sav'), verbose=False)
|
||
|
|
assert_equal(s.array7d.shape, (2, 1, 2, 3, 4, 3, 2))
|
||
|
|
assert_(np.all(s.array7d == np.float32(4.)))
|
||
|
|
assert_(np.all(vect_id(s.array7d) == id(s.array7d[0,0,0,0,0,0,0])))
|
||
|
|
|
||
|
|
def test_8d(self):
|
||
|
|
s = readsav(path.join(DATA_PATH, 'array_float32_pointer_8d.sav'), verbose=False)
|
||
|
|
assert_equal(s.array8d.shape, (4, 3, 2, 1, 2, 3, 5, 4))
|
||
|
|
assert_(np.all(s.array8d == np.float32(4.)))
|
||
|
|
assert_(np.all(vect_id(s.array8d) == id(s.array8d[0,0,0,0,0,0,0,0])))
|
||
|
|
|
||
|
|
|
||
|
|
class TestPointerStructures:
|
||
|
|
# Test that structures are correctly read in
|
||
|
|
|
||
|
|
def test_scalars(self):
|
||
|
|
s = readsav(path.join(DATA_PATH, 'struct_pointers.sav'), verbose=False)
|
||
|
|
assert_identical(s.pointers.g, np.array(np.float32(4.), dtype=np.object_))
|
||
|
|
assert_identical(s.pointers.h, np.array(np.float32(4.), dtype=np.object_))
|
||
|
|
assert_(id(s.pointers.g[0]) == id(s.pointers.h[0]))
|
||
|
|
|
||
|
|
def test_pointers_replicated(self):
|
||
|
|
s = readsav(path.join(DATA_PATH, 'struct_pointers_replicated.sav'),
|
||
|
|
verbose=False)
|
||
|
|
assert_identical(s.pointers_rep.g,
|
||
|
|
np.repeat(np.float32(4.), 5).astype(np.object_))
|
||
|
|
assert_identical(s.pointers_rep.h,
|
||
|
|
np.repeat(np.float32(4.), 5).astype(np.object_))
|
||
|
|
assert_(np.all(vect_id(s.pointers_rep.g) == vect_id(s.pointers_rep.h)))
|
||
|
|
|
||
|
|
def test_pointers_replicated_3d(self):
|
||
|
|
s = readsav(path.join(DATA_PATH, 'struct_pointers_replicated_3d.sav'),
|
||
|
|
verbose=False)
|
||
|
|
s_expect = np.repeat(np.float32(4.), 24).reshape(4, 3, 2).astype(np.object_)
|
||
|
|
assert_identical(s.pointers_rep.g, s_expect)
|
||
|
|
assert_identical(s.pointers_rep.h, s_expect)
|
||
|
|
assert_(np.all(vect_id(s.pointers_rep.g) == vect_id(s.pointers_rep.h)))
|
||
|
|
|
||
|
|
def test_arrays(self):
|
||
|
|
s = readsav(path.join(DATA_PATH, 'struct_pointer_arrays.sav'), verbose=False)
|
||
|
|
assert_array_identical(s.arrays.g[0],
|
||
|
|
np.repeat(np.float32(4.), 2).astype(np.object_))
|
||
|
|
assert_array_identical(s.arrays.h[0],
|
||
|
|
np.repeat(np.float32(4.), 3).astype(np.object_))
|
||
|
|
assert_(np.all(vect_id(s.arrays.g[0]) == id(s.arrays.g[0][0])))
|
||
|
|
assert_(np.all(vect_id(s.arrays.h[0]) == id(s.arrays.h[0][0])))
|
||
|
|
assert_(id(s.arrays.g[0][0]) == id(s.arrays.h[0][0]))
|
||
|
|
|
||
|
|
def test_arrays_replicated(self):
|
||
|
|
s = readsav(path.join(DATA_PATH, 'struct_pointer_arrays_replicated.sav'),
|
||
|
|
verbose=False)
|
||
|
|
|
||
|
|
# Check column types
|
||
|
|
assert_(s.arrays_rep.g.dtype.type is np.object_)
|
||
|
|
assert_(s.arrays_rep.h.dtype.type is np.object_)
|
||
|
|
|
||
|
|
# Check column shapes
|
||
|
|
assert_equal(s.arrays_rep.g.shape, (5, ))
|
||
|
|
assert_equal(s.arrays_rep.h.shape, (5, ))
|
||
|
|
|
||
|
|
# Check values
|
||
|
|
for i in range(5):
|
||
|
|
assert_array_identical(s.arrays_rep.g[i],
|
||
|
|
np.repeat(np.float32(4.), 2).astype(np.object_))
|
||
|
|
assert_array_identical(s.arrays_rep.h[i],
|
||
|
|
np.repeat(np.float32(4.), 3).astype(np.object_))
|
||
|
|
assert_(np.all(vect_id(s.arrays_rep.g[i]) == id(s.arrays_rep.g[0][0])))
|
||
|
|
assert_(np.all(vect_id(s.arrays_rep.h[i]) == id(s.arrays_rep.h[0][0])))
|
||
|
|
|
||
|
|
def test_arrays_replicated_3d(self):
|
||
|
|
pth = path.join(DATA_PATH, 'struct_pointer_arrays_replicated_3d.sav')
|
||
|
|
s = readsav(pth, verbose=False)
|
||
|
|
|
||
|
|
# Check column types
|
||
|
|
assert_(s.arrays_rep.g.dtype.type is np.object_)
|
||
|
|
assert_(s.arrays_rep.h.dtype.type is np.object_)
|
||
|
|
|
||
|
|
# Check column shapes
|
||
|
|
assert_equal(s.arrays_rep.g.shape, (4, 3, 2))
|
||
|
|
assert_equal(s.arrays_rep.h.shape, (4, 3, 2))
|
||
|
|
|
||
|
|
# Check values
|
||
|
|
for i in range(4):
|
||
|
|
for j in range(3):
|
||
|
|
for k in range(2):
|
||
|
|
assert_array_identical(s.arrays_rep.g[i, j, k],
|
||
|
|
np.repeat(np.float32(4.), 2).astype(np.object_))
|
||
|
|
assert_array_identical(s.arrays_rep.h[i, j, k],
|
||
|
|
np.repeat(np.float32(4.), 3).astype(np.object_))
|
||
|
|
g0 = vect_id(s.arrays_rep.g[i, j, k])
|
||
|
|
g1 = id(s.arrays_rep.g[0, 0, 0][0])
|
||
|
|
assert np.all(g0 == g1)
|
||
|
|
h0 = vect_id(s.arrays_rep.h[i, j, k])
|
||
|
|
h1 = id(s.arrays_rep.h[0, 0, 0][0])
|
||
|
|
assert np.all(h0 == h1)
|
||
|
|
class TestTags:
|
||
|
|
'''Test that sav files with description tag read at all'''
|
||
|
|
|
||
|
|
def test_description(self):
|
||
|
|
s = readsav(path.join(DATA_PATH, 'scalar_byte_descr.sav'), verbose=False)
|
||
|
|
assert_identical(s.i8u, np.uint8(234))
|
||
|
|
|
||
|
|
|
||
|
|
def test_null_pointer():
|
||
|
|
# Regression test for null pointers.
|
||
|
|
s = readsav(path.join(DATA_PATH, 'null_pointer.sav'), verbose=False)
|
||
|
|
assert_identical(s.point, None)
|
||
|
|
assert_identical(s.check, np.int16(5))
|
||
|
|
|
||
|
|
|
||
|
|
def test_invalid_pointer():
|
||
|
|
# Regression test for invalid pointers (gh-4613).
|
||
|
|
|
||
|
|
# In some files in the wild, pointers can sometimes refer to a heap
|
||
|
|
# variable that does not exist. In that case, we now gracefully fail for
|
||
|
|
# that variable and replace the variable with None and emit a warning.
|
||
|
|
# Since it's difficult to artificially produce such files, the file used
|
||
|
|
# here has been edited to force the pointer reference to be invalid.
|
||
|
|
with warnings.catch_warnings(record=True) as w:
|
||
|
|
warnings.simplefilter("always")
|
||
|
|
s = readsav(path.join(DATA_PATH, 'invalid_pointer.sav'), verbose=False)
|
||
|
|
assert_(len(w) == 1)
|
||
|
|
assert_(str(w[0].message) == ("Variable referenced by pointer not found in "
|
||
|
|
"heap: variable will be set to None"))
|
||
|
|
assert_identical(s['a'], np.array([None, None]))
|
||
|
|
|
||
|
|
|
||
|
|
def test_attrdict():
|
||
|
|
d = _idl.AttrDict({'one': 1})
|
||
|
|
assert d['one'] == 1
|
||
|
|
assert d.one == 1
|
||
|
|
with pytest.raises(KeyError):
|
||
|
|
d['two']
|
||
|
|
with pytest.raises(AttributeError, match='has no attribute'):
|
||
|
|
d.two
|